The Extracellular Matrix Interaction DataBase
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ExtraCellular Matrix ressources
  • MatrixDB biomolecules
  • MatrixDB annotated sets
  • The matrisome project
  • Laminin
  • Osteogenesis imperfecta
  • Specific subnetworks
  • Collagen maps
  • Adhesomes
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MatrixDB is a freely available database focused on interactions established by extracellular proteins and polysaccharides

MatrixDB stores experimental data established by full-length proteins, matricryptins, glycosaminoglycans, lipids and cations.
MatrixDB reports interactions with individual polypeptide chains or with multimers (e.g. collagens, laminins, thrombospondins) when appropriate. Multimers are treated as permanent complexes, referencing EBI identifiers when possible. Human interactions were inferred from non-human homologous interactions when available.

MatrixDB is an active member of the International Molecular Exchange (IMEx) consortium. Experiments are reported according to the Minimum Information required for reporting a Molecular Interaction experiment (MIMIx, Orchard et al. 2007 Nat Biotechnol. PubMed) or to the International Molecular Exchange curation rules (IMEx, Orchard et al. 2012 Nat Methods. PubMed). As an IMEx member, MatrixDB uses the PSI-MI controlled vocabulary.


The MatrixDB web-interface provides an interactive access to a core of data curated in-house, enriched with ECM-associated interactions provided by IMEx partners (DIP, InnateDB, IntAct, MINT).
Additionaly, all the data curated by MatrixDB are provided for programmatic access through a PSICQUIC webservice.

MatrixDB is in charge of the curation of papers published in Matrix Biology since January 2009.


If you use these data, please cite the following reference:
MatrixDB, the extracellular matrix interaction database. Chautard E et al. 2011 Nucleic Acids Res. (Database issue) PubMed

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Building and exploring interaction networks

iNavigator, our new interaction network browser, allows to construct networks using as entry point any publication, biomolecule or annotation term. iNavigator runs in your browser and communicates with the MatrixDB server. Interaction and biomolecule data are retrieved on the fly and incrementally added to your network.
The network navigator is compatible with these web browsers

Getting started: play with selected interactoms

  • The endostatin interaction network. Faye et al. 2009 J Biol Chem. PubMed
  • The procollagen C-proteinase enhancer-1 extracellular interaction network. Salza et al. 2014 Biochem. J. PubMed
  • The elastic fiber interactome. Cain et al. 2009 Mol Cell Proteomics. PubMed

Beyond iNavigator

iNavigator can export your network at any time in the widely used sif format. You can then leverage the full power of tools such as Cytoscape to further analyse your network.

MatrixDB biomolecule entries

Proteins
They are identified by their UniProtKB/Swiss-Prot primary Accession Number (Example: P98160). This is the most stable identifier of UniProtKB/Swiss-Prot (when a protein entry is modified, the previous accession number is retained in a secondary accession number list).
Multimers
They are identified by a MatrixDB-specific identifier "MULT_x_species" or "MULT_x_VARy_species" for molecular isoforms where x and y are numbers. A cross-reference to EBI complexes is provided when available.
Glycosaminoglycans
They are identified by a MatrixDB-specific identifier "GAG_x" where x is a number. A cross-reference to ChEBI (Chemical Entities of Biological Interest) is provided when available.
Protein fragments
PFRAG in short-form, they are identified by a MatrixDB-specific identifier "PFRAG_x_species" where x is a number. A cross-reference to the PRO feature of UniProtKB is provided when available.
Cations
They are identified by a MatrixDB-specific identifier "CAT_x" where x is a number. A cross-reference to ChEBI (Chemical Entities of Biological Interest) is provided when available.
Lipidic molecules
Fatty-acid related biomolecules are identified by a MatrixDB-specific identifier "LIP_x" where x is a number. A cross-reference to ChEBI (Chemical Entities of Biological Interest) is provided when available.
Synthetic peptides
Engineered peptides are identified by a MatrixDB-specific identifier "SPEP_x" where x is a number. A cross-reference to ChEBI (Chemical Entities of Biological Interest) or an EBI identifier is provided when available.
Others
Remaining molecules are identified by a MatrixDB-specific identifier "INORG_x" where x is a number. A cross-reference to ChEBI (Chemical Entities of Biological Interest) is provided when available.

MatrixDB annotated sets

Lists of human extracellular matrix, secreted and membrane proteins stored in MatrixDB are provided here. They are built based on the Matrisome Project as well as relevant Interactions involving these proteins are extracted using psicquic to enrich the MatrixDB core dataset. UniProt keywords and Gene Ontology terms.

The matrisome

  • Overview of the matrisome - an inventory of extracellular matrix constituents and functions. Hynes et al. 2012 Cold Spring Harb Perpsect Biol. PubMed.
  • Towards definition of an ECM parts list: An advance on GO categories. Naba et al. 2012 Matrix Biology. PubMed.
  • The matrisome: in silico definition and in vivo characterization by proteomics of normal and tumor extracellular matrices. Naba et al. 2012 Mol Cell Proteomics. PubMed
  • Download the human and murine matrisomes from the Hynes Lab

ECM-related databases

Specific extracellular interactomes

  • Extended interaction network of Procollagen C-Proteinase Enhancer-1 in the extracellular matrix. Salza et al. 2013 Biochem J. PubMed
  • Interaction networks as a tool to investigate the mechanisms of aging. Chautard et al. 2010 Biogerontology. PubMed
  • Interaction networks: from protein functions to drug discovery, A review. Chautard et al. 2009 Pathol Biol. PubMed
  • The first draft of the endostatin network. Faye et al. 2009 J. Biol Chem. PubMed
  • The elastic fiber interactome. Cain et al. 2009 Mol Cell Proteomics. PubMed
  • A cell surface interaction network of neural leucine-rich repeat receptors. Söllner et al. 2009 Genome Biol. PubMed
  • The extracellular LRR and IgSF neuroreceptor interaction network. Bushell et al. 2008 Genome Res. PubMed

Interaction maps of collagens


Adhesomes

  • Proteomic analysis of α4 β1 integrin adhesion complexes reveals α-subunit-dependent protein recruitment. Byron A et al. 2012 Proteomics. PubMed
  • The switchable integrin adhesome. Zaidel-Bar R 2010 J Cell Sci. PubMed
  • Network analysis of cell adhesion: adhesomes as context-defined subnetworks. Paris L et al. 2009 Commun Integr Biol. PubMed
  • Proteomic analysis of integrin-associated complexes identifies RCC2 as a dual regulator of Rac1 and Arf6. Humphries JD et al. 2009 Sci Signal. PubMed
  • Functional atlas of the integrin adhesome. Zaidel-Bar R et al. 2007 Nat Cell Biol. PubMed

Video Tutorials

Frequently Asked Questions

What is an interaction?
It refers to a molecular interaction between two molecules. It is supported by a set of experimental evidences. It is identified by a MatrixDB interaction identifier: identifiers (UniProtKB accession number for proteins and MatrixDB identifiers for other molecules) of the participants, separated by an underscore in alphabetical order.
How are experimental evidences indexed?
MatrixDB uses the following naming convention for experiments: identifiers of the biomolecules in alphabetical order separated by two underscore, followed by the PMID (PubMed Identifier), the name of the source database and the number of the experiment (1 for the first reported experiment).

Contact

Visit the Extracellular Interaction Network Lab
Prof. Sylvie RICARD-BLUM
BMSSI, UMR 5086 CNRS - University Lyon 1
Institut de Biologie et Chimie des Protéines
69367 Lyon Cedex 07 - France

Citations

  • The MIntAct project--IntAct as a common curation platform for 11 molecular interaction databases. Orchard S et al. 2014 Nucleic Acids Res. PubMed
  • Protein interaction data curation: the International Molecular Exchange (IMEx) consortium. Orchard S et al. 2012 Nat Methods. PudMed
  • PSICQUIC and PSISCORE: accessing and scoring molecular interactions. Aranda et al. 2011 Nat Methods. PubMed
  • MatrixDB, the extracellular matrix interaction database. Chautard E et al. 2011 Nucleic Acids Res. (Database issue). PubMed
  • MatrixDB, a database focused on extracellular protein-protein and protein-carbohydrate interactions. Chautard E et al. 2009 Bioinformatics. PubMed